Movie Plot:The film concerns the potential outbreak of a Fourth Great Shinobi World War when ninja with kekkei genkai abilities begin to disappear from Kumogakure, Iwagakure, Kirigakure, and Sunagakure.

Team Kakashi is sent on a mission to follow the tracks of the missing kekkei genkai-wielding ninja, which leads them to Mount Shumisen, located between the Land of Earth and Kusagakure. Sai, who is flying on his ink bird, is attacked by a bird which attacks with exploding tag-like feathers, which destroys his bird and makes him fall. Naruto, disobeying Kakashi's orders to continue the mission, runs towards where Sai fell, saying he will not abandon Sai. There, chimera-like creatures attack them which they quickly defeat, although Naruto is injured in the process.

Back at Konoha, Kakashi gives a report on the mission to Tsunade, while worrying that the next ninja targeted will be him. Tsunade seems to not care so much, telling Kakashi to relax. At the hospital, Kakashi gives Naruto his bells, which they used for their first drill together, and tells him to fix them because he crushed them.

Konoha ANBU are sent to Mount Shumisen by Tsunade to search the area for tracks of the missing kekkei genkai ninja. There, a mysterious ninja along with his followers, absorb their chakra with an unknown technique using their Earth nature affinity against them.

That night, the same mysterious ninja, the mastermind and antagonist of the film known as Hiruko, projects his image over the skies of the Five Great Ninja Villages, introducing himself as a shinobi of Konohagakure. He states he that he has taken the kekkei genkai of the four missing ninja using the Chimera Technique, and that he plans to gain the fifth and final kekkei genkai which will make him immortal. By doing so, he declares the Fourth Great Shinobi World War. Konohagakure is believed to be behind the incident, as by the way Hiruko introduced himself, it seems that Konoha is using (or working with) Hiruko. Rumors circulate that they are preparing a rebellion. With the other nations amassing troops at the Land of Fire's borders, threatening invasion, the Fire Daimyo orders Tsunade to apprehend those responsible and prove Konoha's innocence; in the event of failure, the Land of Fire will be forced to destroy the village in order to preserve world peace.

Tsunade is awaiting Gaara at a secret meeting place to discuss what shall be done. However, on the way there Gaara and his Sunagakure shinobi are attacked by the chimera bird's exploding feathers, which traps them in an avalanche.

At Shumisen, Hiruko is thinking of his plan. He states that the Chimera Technique alone can only absorb a maximum of four kekkei genkai, and that certain conditions, most importantly the light af an annular eclipse (which is two days away), are required for the absorption of the fifth and final kekkei genkai, which will make him immortal. That night, Hiruko appears before Kakashi in a dream, activating the Puppet Curse he had placed on him over ten years ago, planning to steal Kakashi's Sharingan. Kakashi asks Tsunade to allow him to go, for the sake of the village. Before he leaves, Kakashi asks Tsunade to place a special seal on him which will automatically activate Kamui when Hiruko attempts to absorb him.

The same night, Shikamaru is visiting Asuma's grave while Kakashi is visiting Obito's. Kakashi asks Shikamaru to tell Naruto that he is leaving the village, and not to follow him. As Kakashi lets Hiruko take over his body, Naruto sees him and chases him. Shikamaru stops him and tells him what Kakashi told him to say. At the Hokage's office, Tsunade orders Konoha 11 to stay away from Kakashi, labelling him as a missing-nin for the sake of the secret mission. After the others leave, Tsunade tells Shikamaru the truth, trusting that he will do what he needs to do as the leader. Meanwhile, Sakura comes to rescue Naruto from the cell that Shikamaru put him in, then they leave the village to rescue Kakashi. Konoha 11 is sent to retrieve them.

The next day, Sunagakure is lining up troops and weapons at the borders of the Land of Fire, thinking that Konoha attacked Gaara, their Kazekage.

Naruto and Sakura are following Kakashi, and witness him passing through a gate. At the same time, the Konoha 11 meet up with Naruto and Sakura, and try to bring them back. Naruto reveals what he learned from Kakashi: "Although shinobi who abandon their mission are considered scum, shinobi who abandon their friends are even lower then scum," which changes the minds of some members. However the scene is interrupted by Ichi, who was sent by Hiruko to stop and/or delay them, using his chimera snakes. Team Guy stays behind to allow the others to pass through the first gate.

At some point, Naruto and Sakura gain a distance from the others, and continue forward as Shikamaru and other members of Konoha 11 follow them. Ni and her chimera nin-dogs stop them at the next gate, and Team 8 stays behind to delay her, while Naruto and Sakura, and later Team 10, pass.

As Naruto, Sakura, and Team 10 reach the next gate, San appears riding the bird that molts exploding feathers. Team 10 is still following the original mission, and tries to stop Naruto and Sakura. However, Sai appears on his ink bird, using a flash bomb to create a distraction, and takes Naruto and Sakura with him, leaving Team 10 behind to fight San.

At this point, Rock Lee and Neji defeat Ichi using Front Lotus: Eight Trigrams Palms Heavenly Spin while Tenten distracts him, and Team 8 defeats Ni using Secret Technique: Insect Sphere inside a trap that Shino built while Kiba and Hinata delayed her. Team 10 gains an advantage over San, with Shikamaru binding him with his shadow and Ino using the Mind Body Switch Technique to take over his mind to tell him that they are after Naruto, not Kakashi. They also ask him where Kakashi is headed. However, San breaks out of the Mind Body Switch Technique. He then summons Ichi and Ni, uses the Chimera Technique on them and himself, and the three become a huge chimera, which seems to be a combination of all their respective chimera beasts, possessing all of their abilities.

Meanwhile, Gaara is thinking of what Jiraiya said while aiding in the recovery of Gaara and the Suna-nin. He has told Gaara that he believes Kakashi, or even Naruto, will defeat Hiruko, and it is up to Gaara depending on whether he believes in Naruto's strength or not. As the war between Konoha and Suna is about to begin, Jiraiya appears above Gamabunta and gives to Suna the proof that Gaara is still alive. At that moment, Gaara moves to where Naruto, Sakura, and Sai are headed and stops them. He says Naruto's will is not what Kakashi wants, and Naruto begins to fight Gaara. Gaara states that Naruto is too idealistic, that he doesn't have the power to make his goals become true. However, Naruto strongly says by the belief that as a fellow comrade, he cannot allow Kakashi to sacrifice himself. Naruto breaks through Gaara's Shield of Sand, and punches him.

The rest of the members of Konoha 11 arrive to aid Team 10, and they bind the chimera beast, with the help of Tenten, by sending their chakra to the chains that were holding the beast, they asked Shikamaru to go and stop Naruto, Sai and Sakura. Shikamaru meets Gaara, who tells him that he felt what Naruto feels in the battle. Shikamru continues on. Meanwhile, Naruto reaches the final gate, and realizes this is the place they came to on their mission. Naruto goes to Kakashi and tries to stop him, but Kakashi walks on with no response. When Naruto grabs his arm, he sees the seal on his wrist, and Sai tells him what it is. Shikamaru, who has finally caught up to them, reveals that Tsunade placed the seal on him, so that they may defeat Hiruko at the sacrifice of Kakashi. Kakashi passes through the final gate before the temple.

As Naruto, Sakura, Sai, and Shikamaru approach the temple, Naruto hears Hiruko's voice, and questions why he did this, and Hiruko answers by telling a story. He says he was a former friend of the Sannin, but he was not a skilled shinobi like they were. He was developing the Chimera Technique, a jutsu that would allow him to create a synthetic body by combining several separate ones. After the Third Great Shinobi World War, he was shocked when he saw Kakashi, not only because he had survived the battle, but because he had received the Sharingan, a kekkei genkai, from the original user, Obito Uchiha. This gave Hiruko the idea to steal kekkei genkai to become powerful like the Sannin. However, the Hokage found out about his research, and Hiruko was forced to flee.

As Kakashi reaches the temple, Hiruko appears from the shadows of the temple, and welcomes Kakashi. Seeing it as the only way to save Kakashi, Naruto, Sakura, and Sai try to defeat Hiruko although Shikamaru tries to stop them. Hiruko, using his four kekkei genkai: Storm Release, Dark Release, Steel Release, and Swift Release, defeat them with little effort. He then steps into the temple with Kakashi. Naruto stands up, deciding that he cannot give up. Shikamaru tries to stop him, that he must protect the unborn children of Konoha, the "King". Naruto states that he'll protect them too, and that he loves Konoha for its shinobi, who will sacrifice themselves to save one another. However, deciding who will be sacrificed from the start isn't what Naruto wants, and Naruto believes there is no future for the children if Konoha becomes a place like this. As Naruto walks away, Shikamaru sees Asuma in him, and protects him from surrounding exploding tags with his Shadow Sewing Technique, trusting the future of Konoha with him.

Naruto enters the temple, where Hiruko begins the absorption at the beginning of the eclipse. Suddenly, Kakashi's Mangekyō Sharingan activates, and the space inside the slime created by the Chimera technique begins to distort. Naruto, trying to save Kakashi, breaks into the slime with multiple Rasengans and pulls him out. Kakashi wakes up, and sighs that the plan failed. Hiruko is still alive, and he states that the eclipse hasn't ended yet, and releases a large amount of chakra, reducing the surrounding area to rubble. Hiruko then summons the chimera beast that Konoha 11 was keeping restrained, Shikamaru, Sakura, and Sai fight the beast while Naruto and Kakashi face Hiruko. Shikamaru notes that Hiruko's weak spot is his chest, which is still hollow as it is the space that Hiruko wants to assimilate Kakashi into. As the chimera beast begins to gain an advantage over them, Konoha 11 arrive, and Chōji uses his Jutsu to become bigger and attacks the beast, followed by Kiba and Akamaru's Dual Piercing Fang which destroys the beast's wings, then from the sky, Hinata and Neji appear and attack the beast with the Eight Trigrams Sixty-Four Palms, Tenten finishes it off by covering its body with a large number of kunai and exploding tags. Meanwhile, Hiruko is gaining an advantage over Naruto and Kakashi, easily absorbing their techniques: the Great Ball Rasengan and Lightning Cutter. As a last resort, Naruto forms the Wind Release: Rasenshuriken, and carries the impact to Hiruko's chest. Hiruko tries to absorb and copy it, but he cannot combine the high level of shape transformation with the high level of nature transformation.

In his final moments, Hiruko, in his original appearance, asks Kakashi what he did wrong. Kakashi tells him that he used others to overcome his weakness, and only tried to become perfect on his own. Hiruko states that is the way that the strong think, and that others who were stronger than him did not want to be his comrade. However, Hiruko then sees his old friends (including Tsunade, Jiraiya, Orochimaru, and the Third Hokage) appear before his eyes, and they tell him that they wanted to help him. Kakashi tells him if he had tried to bond with them, they would've helped him and he shouldn't have tried to do everything by himself. Hiruko then tells Kakashi that was what Kakashi tried to do this time, as he tried to do it by himself, abandoning his comrades. Kakashi admits his mistake, and Hiruko asks him if he finally made a connection, and dies.

Gaara appears before the Suna-nin army, and tells them everything has been solved, and to withdraw. Tsunade and Jiraiya talk about how they were saved, and that the kids are just like when they were young.

At Mount Shumisen, Konoha 11 are celebrating, Kakashi comes and tells them that they did a good job. Kakashi, reminded of Obito, suddenly smiles, and Naruto says that creepy grins out of nowhere aren't cool, and the other teammates think that Kakashi is gay and make comments on the gayness. Naruto is creeped out and starts to run away; Kakashi chases him telling him to stop, saying it is a misunderstanding.